16.2 Example: Fal biota (one-way case)

Let's look at an example of a means plot for a one-way case using biotic data ($p$ = 131 taxa) from the Fal estuary. The data consist of counts of organisms living in benthic sediments obtained from $n$ = 5-7 sites in each of 5 creeks running into the Fal estuary, Cornwall, UK (
 Somerfield et al. (1994a)
 , 
 Somerfield et al. (1994b)
 ). These 5 creeks had differing levels of heavy metals in their sediments, due to historical tin and copper mining in their respective valleys. Interest lies in identifying whether the 5 creeks also differed in their diversity of benthic infauna. The full set of biotic data (macrofauna and also the meiofauna - comprised of nematodes and copepods) are contained in the file 'Fal_all_biotic_taxa.pri', found in the 'Fal_benthic_fauna' folder in 'Examples_P8'.

Start by calculating some univariate diversity measures for each sample. Open the 'Fal_all_biotic_taxa.pri' file in PRIMER 8, then click Analyse > DIVERSE..., take all the defaults and click 'OK'.

This will produce a sheet, called 'Data1' with values for various diversity indices for each of the sampling units.

Calculate a means plot that shows the means $\pm$ 1 standard error for the 5 creeks for each of these diversity measures. From the 'Data1' sheet, click Plots > Means Plot....

Leave all of the defaults and click 'OK'.

The result will be a 'Multi plot' item, that includes 6 individual plots - one for each of the 6 diversity measure variables in the original 'Data1' sheet.

View an individual plot by clicking on it. For example, you can click on the plot in the top left-hand corner of 'MultiPlot1' to see a means plot for the variable of species richness ('S', the number of different taxa). Alternatively, you can click on 'Graph1' in the Explorer tree.

To change the colours, symbols or line types, you can click Graph > Special..., which shows you a dialog with a plethora of options to modify all of these details of your means plot. For example, you can click the 'Key...' button next to the factor to change the colours/symbols, or choose to $\bullet$ Join means, including the option to choose a custom colour for the joining line, like this:

This will yield the following modified plot:

You can also choose to show the means as bars instead. Click Graph > Special..., then (Display Means as > $\bullet$ Bars) and (Error bars > Appearance > $\bullet$ Custom).

This yields the following plot:

Next, we shall consider some multi-factor plots.